Related papers: Analysis of Transition State Theory Rates upon Spa…
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently-proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time Transition-State Theory (TST) limit is identical to…
Thermal quantum time-correlation functions are of fundamental importance in quantum dynamics, allowing experimentally-measurable properties such as reaction rates, diffusion constants and vibrational spectra to be computed from first…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
Grain boundary (GB) properties greatly influence the mechanical, electrical, and thermal response of polycrystalline materials. Most computational studies of GB properties at finite temperatures use molecular dynamics (MD), which is…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
In a previous article [J. Chem. Phys. 138, 084108 (2013)], we showed that the $t\to 0_+$ limit of ring-polymer molecular dynamics (RPMD) rate-theory is also the $t\to 0_+$ limit of a new type of quantum flux-side time-correlation function,…
Markov state models (MSMs) are a powerful tool to analyze and coarse-grain complex dynamical data into interpretable kinetic processes. This capability is particularly important in heterogeneous catalysis, where a medley of reactants and…
In Part I [J. Chem. Phys. 138, 084108 (2013)] we derived a quantum transition-state theory by taking the t->0+ (short-time) limit of a new form of quantum flux-side time-correlation function containing a ring-polymer dividing surface. This…
Coarse graining (CG) is an important task for efficient modeling and simulation of complex multi-scale systems, such as the conformational dynamics of biomolecules. This work presents a projection-based coarse-graining formalism for general…
Coarse-grained molecular dynamics (CGMD) is a technique developed as a concurrent multiscale model that couples conventional molecular dynamics (MD) to a more coarse-grained description of the periphery. The coarse-grained regions are…
The evaluation of nucleation rates from molecular dynamics trajectories is hampered by the slow nucleation time scale and impact of finite size effects. Here, we show that accurate nucleation rates can be obtained in a very general fashion…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
Many single molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
We describe a path-integral molecular dynamics implementation of our recently developed golden-rule quantum transition-state theory (GR-QTST). The method is applied to compute the reaction rate in various models of electron transfer and…
Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated…
Classical transition state theory (TST) is the cornerstone of reaction rate theory. It postulates a partition of phase space into reactant and product regions, which are separated by a dividing surface that reactive trajectories must cross.…
Recent results on QCD thermodynamics are presented. The nature of the T>0 transition is determined, which turns out to be an analytic cross-over. The absolute scale for this transition is calculated. The temperature dependent static…
A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of "macrostates" (e.g. sets of "microstates"), the consequence on…
The definition of the classical transition state theory (TST) as a t= 0+ limit of the flux-side time correlation function relies on the assumption that simultaneous measurement of population and flux is a well defined physical process.…